{"id":"W2169882791","doi":"10.1016/j.gene.2004.12.011","title":"Site interdependence attributed to tertiary structure in amino acid sequence evolution","year":2005,"lang":"en","type":"article","venue":"Gene","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":104,"is_retracted":false,"has_abstract":false,"ca_institutions":"McGill University; Canadian Institute for Advanced Research; Université de Montréal","funders":"Université de Montréal; Canada Research Chairs; Génome Québec","keywords":"Biology; Pairwise comparison; Phylogenetic tree; Sequence (biology); Threading (protein sequence); Context (archaeology); Multiple sequence alignment; Alignment-free sequence analysis; Tree (set theory); Computational biology; Sequence alignment; Phylogenetics; Set (abstract data type); Molecular evolution; Protein tertiary structure; Evolutionary biology; Peptide sequence; Computer science; Genetics; Protein structure; Mathematics; Artificial intelligence; Combinatorics; Paleontology; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007204164,0.0001246903,0.0001037475,0.00004398124,0.00004098686,0.00001103238,0.000161466,0.00009174951,0.00001467588],"category_scores_gemma":[0.00002900873,0.0001232463,0.00003393285,0.00009001212,0.00002629974,0.000001100117,0.0001852351,0.00006102092,0.00002571343],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004631245,"about_ca_system_score_gemma":0.00003198187,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004451797,"about_ca_topic_score_gemma":0.0008932672,"domain_scores_codex":[0.999195,0.00002664347,0.0001554166,0.0003154763,0.00007400756,0.0002334814],"domain_scores_gemma":[0.9996041,0.000002885872,0.00003184811,0.0002523494,0.00004800329,0.00006080962],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00001908882,0.00001156496,0.02393123,0.000003037004,0.00001293236,0.000002129849,0.00009808708,0.0009469446,0.9704303,0.00000680531,0.0003332508,0.004204612],"study_design_scores_gemma":[0.0002430423,0.00007494108,0.1658881,0.00000670187,0.000005856204,0.00001838805,0.00002179154,0.0001152256,0.8245242,0.00006704088,0.008863403,0.00017125],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9958881,0.001598736,0.001724659,0.0003779776,0.0001060358,0.0001415343,0.0001111597,0.000003775285,0.00004807081],"genre_scores_gemma":[0.9951093,0.0000812017,0.003791542,0.0006174858,0.0001944533,0.00001269167,0.00006336237,0.00001067323,0.0001193463],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1459061,"threshold_uncertainty_score":0.502584,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009726490430959822,"score_gpt":0.2389632307348782,"score_spread":0.2292367403039183,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}